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Complex Portal

by io.github.pipeworx-io

Search Complexes

search_complexes
Read-onlyIdempotent

Search the EBI Complex Portal — a manually curated database of stable macromolecular protein complexes — by protein/complex name, gene, GO term, or biological process (e.g. "apoptosis", "SCF", "ribosome"). Returns matching complexes with their accession (e.g. CPX-7762), name, description, and organism. Keyless. Complements UniProt/IntAct/STRING.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoMax results to return (default 15, max 100).
queryYesProtein/complex name, gene, or GO term, e.g. "apoptosis", "SCF", "ribosome".

TDQS

A4.5/5.0
Behavior4/5

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

Annotations already declare readOnlyHint, openWorldHint, idempotentHint, destructiveHint, so the description adds value by noting it's keyless (no auth) and returns specific fields (accession, name, description, organism). No contradictions.

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 two sentences with no wasted words. The first sentence immediately states purpose and query methods, the second adds complementary info (keyless, complements other tools). Highly efficient.

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?

For a simple tool with 2 parameters, no output schema, and no nested objects, the description is complete. It explains what the tool searches, how to query (examples), what it returns, and its relationship to other databases. No gaps.

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% with descriptions for both 'query' and 'limit'. The description enhances meaning by giving example queries ('apoptosis', 'SCF', 'ribosome') and noting the return fields, adding practical context 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 states it searches the EBI Complex Portal for macromolecular protein complexes by name, gene, GO term, or biological process. It specifies the database as curated and lists return fields (accession, name, description, organism), distinguishing it from sibling tools like 'get_complex'.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description indicates it's keyless and complements other databases (UniProt/IntAct/STRING), giving context on when to use it. It doesn't explicitly state when not to use it, but the purpose is clear and no misleading guidance is present.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

All Complex Portal toolsInspect
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TDQS

A3.8/5.0
Disambiguation2/5

Multiple tools have overlapping boundaries: ask_pipeworx and ask_pipeworx_beta are explicitly identical, ask_pipeworx_grounded and deep_research heavily overlap with them, and entity_profile, compare_entities, recent_changes, and validate_claim all circle the same company-data space. The prediction-market cluster (polymarket_edges, polymarket_edge_tracker, polymarket_arbitrage, polymarket_fill_risk, polymarket_kalshi_spread) also requires careful reading to distinguish. The descriptions help, but the set relies on them to disambiguate near-duplicates.

Naming Consistency4/5

Nearly all tools follow a consistent lowercase snake_case style, whether verb_noun (search_complexes, validate_claim, unsubscribe), noun_verb (entity_profile, recent_changes), or brand-like (ask_pipeworx, polymarket_edges). There is no camelCase mixing or chaotic verb style. Minor inconsistency exists between imperative verbs (remember, forget, subscribe) and noun-style names, but the overall pattern is readable and predictable.

Tool Count2/5

33 tools is well above the 25-tool 'heavy' threshold, and many are meta-tools (discover_tools, suggest_questions, pipeworx_feedback, pipeworx_trending, remember/recall/forget) that pad the surface. The server is named 'Complex Portal', yet only two tools serve that purpose—the rest belong to a broad data platform. The count feels inflated and misaligned with the server's stated identity.

Completeness3/5

For the broad Pipeworx data platform the surface is fairly complete: universal querying, grounded answers, deep research, entity profiles, comparisons, claim validation, subscriptions, memory, and feedback. For the Complex Portal domain named by the server, coverage is thin—just search and fetch-by-accession, with no browsing, species filtering, or cross-reference tools. The core workflow works, but the namesake domain is under-served relative to the rest of the set.

Resources