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Biosamples

by io.github.pipeworx-io

Search Samples

search_samples
Read-onlyIdempotent

Search EBI BioSamples — metadata for biological samples (cell lines, tissues, organisms) referenced across EBI archives. Free-text search by organism, tissue, or keyword; returns matching samples with accession, name, organism, and release date. Keyless.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pageNoZero-based page number (default 0).
limitNoMax results to return (default 15, max 100).
queryYesFree-text query — organism, tissue, cell type, or any keyword (e.g. "liver", "Homo sapiens", "cancer cell line").

TDQS

A4/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, idempotentHint=true, and destructiveHint=false, covering safety. The description adds that it returns specific fields (accession, name, organism, release date), but does not detail additional behaviors like rate limits or pagination limits beyond the schema.

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 efficient sentences, front-loaded with the core purpose. Every sentence adds value with no redundancy.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With 100% schema coverage, rich annotations, and no output schema needed, the description covers the tool's functionality well. It could mention pagination behavior beyond defaults, but it's not essential.

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% with clear parameter descriptions. The description reinforces that query is a free-text search but adds no new parameter-level details. Baseline for full coverage is 3.

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 'Search EBI BioSamples' and specifies the type of metadata and search fields (organism, tissue, keyword). It distinguishes from siblings like 'get_sample' which retrieves a single sample.

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 mentions 'Free-text search' and 'Keyless', giving usage context. However, it does not explicitly state when not to use this tool or point to alternatives like 'get_sample' for specific sample retrieval.

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

All Biosamples toolsInspect
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TDQS

A3.8/5.0
Disambiguation2/5

Many tools overlap heavily: ask_pipeworx, ask_pipeworx_beta, and ask_pipeworx_grounded are near-identical variants (beta currently identical), and the set includes five-plus prediction-market tools (polymarket_arbitrage, polymarket_edges, polymarket_edge_tracker, polymarket_fill_risk, polymarket_kalshi_spread, bet_research) with fuzzy boundaries. Long descriptions help, but an agent selecting among them would frequently struggle to pick the right one.

Naming Consistency3/5

Names are uniformly lowercase snake_case, but the pattern is inconsistent: verb_first names (search_samples, validate_claim, resolve_entity) mix with noun-style names (entity_profile, pipeworx_trending, polymarket_arbitrage) and bare imperatives (remember, recall, forget, subscribe). It is readable, but there is no predictable verb_noun convention across the set.

Tool Count2/5

33 tools is well over the coherent range, and the count is especially inflated because the server is named Biosamples yet only two tools (search_samples, get_sample) actually belong to that domain. The remaining 31 tools are an unrelated mix of Pipeworx research, prediction-market, memory, and subscription utilities, including redundant variants.

Completeness2/5

For the stated Biosamples purpose, only search and retrieve exist—no submission, update, or batch operations—so the domain surface is a read-only fragment. For the broader accidental scope of the other tools, the set is a grab bag with no coherent lifecycle, leaving significant gaps regardless of which domain is considered primary.

Resources