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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

A4.9/5.0
Behavior5/5

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

Annotations already declare read-only, idempotent, and non-destructive behavior, and the description adds substantial context: returns a findings packet with evidence, confidence, source, fetched_at, stable citations, explicit gaps[], contradictions[], and never-fabricated answers. It also documents second-hop depth behavior, semantic excerpting, citation resolvability, and timing expectations. No contradiction 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 long, but the length is earned for a complex tool. Critical constraints are front-loaded (account required, not open-web search, ask_pipeworx alternative), followed by behavioral details and timing. Every sentence adds useful decision-relevant information without meaningful 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?

With no output schema, the description carries the full burden of explaining return values and behavior — and it does so thoroughly. It explains what the findings packet contains, how gaps and contradictions are handled, how citations work, what depth levels do, how long to wait, and which sibling to fall back to. This is more than enough 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 description coverage is 100%, so the baseline is 3. The description adds value beyond the schema with concrete example questions, clarifies that multi-part natural language questions are appropriate, and provides practical context on account requirements and latency for depth options. This pushes it above baseline, though the schema already carries most depth semantics.

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 the tool's job: grounded multi-source research across Pipeworx's structured data sources in one call. It explicitly contrasts itself with open-web search and names the sibling alternative (ask_pipeworx), while providing concrete example questions that make its scope easy to distinguish 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?

The description is explicit about when to use this tool (broad/multi-part questions over structured data) and when not to (single lookups should use ask_pipeworx). It also gives account-tier guidance, noting that non-signed-in users should use ask_pipeworx, and explains the depth modes' behavior and expected latency.

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

Several tools have overlapping purposes: ask_pipeworx, ask_pipeworx_beta (currently identical), ask_pipeworx_grounded, deep_research, and validate_claim all handle routed research queries, while ai_visibility_check and scan_competitor_ai_presence overlap directly and the six Polymarket tools form a dense, easily confused cluster. The descriptions are detailed, but an agent will frequently struggle to pick the right tool among near-duplicate research and prediction-market options.

Naming Consistency3/5

Names are readable and mostly snake_case, with useful prefixes like ask_pipeworx_ and polymarket_. However, conventions are mixed: some are verb_noun (search_genes, get_protein, generate_llms_txt), some are bare verbs (remember, recall, forget), and some are noun phrases (entity_profile, recent_changes, top_tissues). There is no single predictable pattern.

Tool Count2/5

34 tools is above the 25+ threshold for a heavy, hard-to-navigate set, and most of them are not related to the server's stated 'Protein Atlas' identity. Only three tools actually concern proteins, while the rest form a general data-research, Polymarket, memory, and subscription toolkit that feels like several servers merged into one.

Completeness2/5

For a Protein Atlas server, the surface is severely incomplete: only search_genes, get_protein, and top_tissues cover HPA, leaving pathology, cell-line, single-cell, blood, and other major HPA dimensions unaddressed. If the intended domain is instead the broader Pipeworx data router, the protein tools are an odd vestige and the completeness story is still muddled by overlapping meta-tools.