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Protein Atlas

by io.github.pipeworx-io

Validate Claim

validate_claim
Read-onlyIdempotent

"Is it true that…" / "fact check" / "verify the claim that…" / "did X really…" / "was Y actually…" / "confirm or refute" / "true or false" — natural-language claim verification against authoritative sources. Use whenever the agent needs to check whether something a user said is factually correct. Company-financial claims (revenue, net income, cash for public US companies) verify via the structured SEC EDGAR + XBRL fast path with exact percent-delta math; ANY OTHER factual claim (macro statistics, rates, prices, drug data, records) automatically falls through to the grounded pipeline — routed to the right live source, answered with verbatim evidence, then judged. Returns a verdict (confirmed / approximately_correct / refuted / inconclusive / unsupported / could_not_verify), the grounded or structured actual value with pipeworx:// citation, and reasoning. IMPORTANT for callers: could_not_verify means the check did not happen (our LLM or source failed) and carries verification_error{stage,detail} — it is NOT evidence for or against the claim, and must not be shown as one. unsupported means we looked and cover no source for it. Replaces 4–6 sequential calls (NL parsing → entity resolution → data lookup → comparison).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
claimYesNatural-language factual claim, e.g., "Apple's FY2024 revenue was $400 billion" or "Microsoft made about $100B in profit last year".
tolerance_pctNoMax percent deviation still graded approximately_correct (0.5–50). Overrides the tolerance implied by the claim wording — set 1–2 for hallucination detection where any material error must be refuted. Default: implied by wording, capped at 5.

Schema Changelog

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

  1. Changed1 schema field changed
    • addedInput schema / properties / tolerance_pct
      Added value: +{
+  "description": "Max percent deviation still graded approximately_correct (0.5–50). Overrides the tolerance implied by the claim wording — set 1–2 for hallucination detection where any material error must be refuted. Default: implied by wording, capped at 5.",
+  "type": "number"
+}
  2. First observed

TDQS

A4.8/5.0
Behavior5/5

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

Annotations already declare readOnly=true, openWorld=true, idempotent=true, and destructive=false, but the description goes well beyond them by explaining the routing logic, the verdict types (confirmed, refuted, etc.), the inclusion of verbatim evidence and a citation, and the critical caveat that 'could_not_verify' is not evidence for or against the claim. This adds significant behavioral context not inferable from 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 densely packed with essential information: example phrases, use-case, routing, return values, caveats, and efficiency note. It is well-structured with semicolons and dashes, but could be slightly tighter without losing meaning. However, every sentence contributes value, so it earns a high score.

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?

Given two simple parameters and no output schema, the description is remarkably complete. It explains return verdicts, the actual value with citation, reasoning, the meaning of error states, the routing logic for different claim types, and the alternative to sequential calls. For a tool of this complexity, nothing essential is missing.

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?

The schema already has 100% coverage with descriptions for both parameters. The description adds extra nuance by explaining how tolerance_pct overrides the claim's implied wording tolerance, mentions the default cap of 5%, and recommends 1–2% for hallucination detection. This goes beyond the schema's bare numeric range, though it doesn't fully redefine the 'claim' parameter beyond the schema's examples.

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 opens with concrete example phrasings and states the core function: 'natural-language claim verification against authoritative sources.' It clearly distinguishes the tool from siblings by specifying the fact-checking use case and the two distinct pipelines (SEC EDGAR for company-financial claims, grounded pipeline for anything else), which separates it from general-purpose tools like ask_pipeworx or deep_research.

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 'Use whenever the agent needs to check whether something a user said is factually correct.' It further differentiates when the structured SEC path applies versus the grounded fallback, and warns about the meaning of 'could_not_verify' vs 'unsupported,' giving clear guidance on interpreting results. It also notes this replaces multiple sequential calls, reinforcing when to select it.

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.

Resources