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Biostudies

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 1500 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 5,743 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.

TDQS

A4.8/5.0
Behavior5/5

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

Highly transparent: discloses account/plan requirements, parallel facet decomposition, explicit gaps[] behavior ('never invented'), stable pipeworx:// citations, contradictions[] for standard/thorough, hop fields, and semantic excerpting of large records. It also clearly states 'this is NOT open-web search'. No contradiction with the readOnly/openWorld/idempotent 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 long but front-loaded with the account requirement and core identity, then flows into usage alternatives and depth-specific behavior. Every sentence carries operational weight, though a few details (e.g., citation_uri semantics) are dense and could be streamlined. Overall, well-structured and earns its length.

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 fully carries the burden of explaining return values: findings packet with verbatim evidence, confidence, source, fetched_at, citation, gaps[], contradictions[], hop field, and citation_uri. It also covers auth, pricing, latency, and failure behavior. For a tool with this complexity, it is exceptionally complete.

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. The description adds meaningful context beyond the schema: depth is tied to paid plans and hop counts, question examples ('compare X and Y's regulatory + financial exposure') clarify expected input, and the 'broad/multi-part is fine' note enriches the question parameter. This pushes it above baseline.

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 action (grounded multi-source research), a precise resource (Pipeworx's 1500 structured data sources via 5,743 tools in parallel), and explicitly differentiates itself from open-web search and sibling ask_pipeworx. The verb 'decomposes' plus the detailed output packet make the tool's function unambiguous.

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/when-not guidance: use ask_pipeworx if not signed in, for a single lookup, or for breaking/live news; use deep_research for broad/multi-part structured-data questions. It also differentiates depth levels ('standard' adds gap recovery, 'thorough' adds lead chasing and contradictions) and notes latency expectations.

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 occupy nearly identical roles: ask_pipeworx and ask_pipeworx_beta are described as functionally identical right now, ask_pipeworx_grounded and deep_research are overlapping query modes, and ai_visibility_check / scan_competitor_ai_presence / discover_tools / suggest_questions all blur into discovery or visibility tasks. The two actual BioStudies tools are clear, but they are buried in a server dominated by Pipeworx meta-tools.

Naming Consistency3/5

All tool names use snake_case, and many follow a verb_noun shape such as search_studies, get_study, and discover_tools. However, the convention is inconsistent across the set: noun-first names like entity_profile and polymarket_edges, brand-prefixed names like pipeworx_feedback, and verb-first product names like ask_pipeworx all coexist, making the pattern harder to predict.

Tool Count2/5

33 tools is well into the too-many range, and the count is especially inappropriate for a server named Biostudies since only search_studies and get_study actually belong to that domain. The rest form a sprawling general-purpose data-research platform that appears to have been merged into one server without a clear scope.

Completeness3/5

For the BioStudies-specific surface, search_studies and get_study provide reasonable read-only coverage for the EBI archive. But as the broader research platform the other 31 tools imply, the set is hard to evaluate for completeness because most actual data access is delegated to Pipeworx's hidden 5,718 tools rather than exposed directly, leaving notable gaps in transparency and direct source-level control.

Resources