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Plos

by io.github.pipeworx-io

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

A4.6/5.0
Behavior5/5

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

The description goes well beyond the readOnly/openWorld annotations by disclosing account tier requirements, latency expectations, gap reporting, never-invented behavior, citation fetchability guarantees, and semantic excerpting behavior. It also explains depth-specific behaviors like contradiction scans and gap recovery without contradicting any annotation.

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 long but dense, front-loading the critical account requirement and alternative tool before detailed mechanics. Some depth details are duplicated from the schema, and the punctuation-heavy flow could be cleaner, but every sentence carries substantive content.

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 findings packet structure, evidence fields, citations, gaps, contradictions, latency, and auth constraints. For a complex parallel-research tool, this is unusually complete.

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% and the schema already fully documents the depth enum and the question parameter. The description restates some depth behavior and adds latency context, but does not add meaningfully new parameter-level semantics beyond 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 clearly identifies the tool as grounded multi-source research over Pipeworx's 1517 structured data sources, with explicit contrast to open-web search. It also distinguishes itself from sibling ask_pipeworx by stating it decomposes broad multi-part questions and runs parallel tool calls.

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 explicitly says to use ask_pipeworx when not signed in and for single lookups, and states that deep_research is best for broad/multi-part questions over structured data. This gives clear when-to-use, when-not-to-use, and alternative guidance.

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

B3.2/5.0
Disambiguation2/5

Several tools have overlapping purposes: ask_pipeworx, ask_pipeworx_beta, and ask_pipeworx_grounded are near-identical in function, while compare_entities and entity_profile both fan out across data sources. The PLOS-specific tools (article, search, recent) are distinct, but the broader set creates confusion about which entry point to use for general data questions.

Naming Consistency2/5

The naming is a mix of single-word nouns (article, recent), verb phrases (search_authored_by, validate_claim), and adjective_noun constructions (recent_changes, recent_alerts). While most multi-word names use snake_case, the lack of a consistent prefix or verb_pattern (e.g., some start with action verbs, others with data categories like polymarket_ or pipeworx_) makes the set feel inconsistent.

Tool Count2/5

At 35 tools, the server is heavily over-scoped for a PLOS journal interface—only 4 tools (article, search, search_authored_by, recent) actually relate to PLOS. The remaining 31 tools form a broad Pipeworx/Polymarket data platform, which suggests the server is trying to do far more than its name implies.

Completeness2/5

For the stated domain (PLOS), the surface is thin: basic search, fetch, recent, and author search lack advanced features like citation metrics, journal browsing, or full-text download links. Conversely, the Pipeworx tools are extensive but unrelated to PLOS, so the set is simultaneously over-complete in unrelated areas and incomplete for its apparent purpose.

Resources