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Expression Atlas

by io.github.pipeworx-io

Search Experiments

search_experiments
Read-onlyIdempotent

Search EBI Expression Atlas — ~4,500 curated gene/protein expression experiments (baseline & differential) across species, tissues, and conditions. Filter by keyword (matches description/experimental factors), species (e.g. "Homo sapiens", "Mus musculus"), and/or type ("Baseline" or "Differential"). Returns accession, description, species, type, assay count, and factors. Keyless. Complements UniProt/Ensembl.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
typeNoExperiment type: "Baseline" or "Differential".
limitNoMax results (default 25, max 100).
queryNoKeyword matched (case-insensitive) against experiment description OR any experimental factor, e.g. "liver", "stress", "cancer".
speciesNoSpecies substring (case-insensitive), e.g. "Homo sapiens", "Mus musculus", "Arabidopsis thaliana".

TDQS

A4.1/5.0
Behavior3/5

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

Annotations already declare readOnlyHint, idempotentHint, etc. Description adds return fields and keyless access, but no further behavioral traits. Consistent with annotations, no contradiction.

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?

Two sentences, both front-loaded with key information. No fluff, every sentence earns its place.

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 no output schema, description enumerates return fields (accession, description, species, type, assay count, factors). Includes count, types, and keyless nature. Complete for a search tool.

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 description coverage is 100%. Description adds case-insensitive filtering, but largely restates schema info (e.g., type, species, query). No additional semantics beyond 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?

Clearly states the tool searches the EBI Expression Atlas for gene/protein expression experiments. Specifies the resource, count (~4,500 curated experiments), and types (baseline & differential). Distinguishes from siblings like 'get_experiment' and complements 'UniProt/Ensembl'.

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?

Provides context on when to use (for expression data) and names complementary tools. Implicitly suggests alternatives by noting it complements UniProt/Ensembl, but lacks explicit when-not-to-use or exclusion criteria.

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

All Expression Atlas toolsInspect
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TDQS

A3.7/5.0
Disambiguation3/5

Many tools have overlapping purposes (e.g., multiple Polymarket tools, multiple company information tools), but descriptions help distinguish them. However, the variety of domains (brand monitoring, betting, package scanning, memory, etc.) can confuse an agent.

Naming Consistency2/5

Tool names have no consistent naming pattern: some are verb_noun (validate_claim), some are noun_verb (bet_research), some are compound (ai_visibility_check), and some are single word (forget). This makes it hard to predict tool names.

Tool Count2/5

28 tools is high, and the set spans many unrelated domains (brand visibility, SEC/FDA data, Polymarket, npm packages, memory, etc.) while the server is named 'Expression Atlas' with only 2 tools related to that purpose. The tool count feels excessive and unfocused.

Completeness1/5

For a server named 'Expression Atlas', only two tools (get_experiment, search_experiments) cover the domain. There are no tools for submitting, updating, or deleting experiments, nor any for data visualization. The surface is severely incomplete.

Resources