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select_assays

Read-onlyIdempotent

List experimental groups for a study and resolve a factor pair into matching assay identifiers with technology and measurement details.

Instructions

USE THIS TOOL (not the query tool) for ANY question about the groups a study contains, and to resolve a factor-pair condition into the matching assay identifier(s):

"What groups / conditions / control and experimental (treatment) groups are in OSD-48?", "which comparisons or factors does this study have?", "what was compared against what?" — call with just study_id (list mode). The numbered factor menu it returns IS the list of groups: each entry is one experimental group (a set of factor values such as "Space Flight,Carcass"), and each assay is a comparison of two such groups (condition 1 vs condition 2, e.g. experimental vs control). Never use query for this.
"Give me the assay for Space Flight,Carcass vs Ground Control,Carcass" — call with study_id and selection to resolve that factor pair (e.g. "2,1") into assay identifier(s).

Falling back to query for this category loses the numbered factor menu, the per-match technology/measurement/method columns, and the next-step suggestions this tool emits.

List and select assays for a study and render the response in markdown format.

First call (selection=None):

If study_id missing, prompt for one (e.g., 'OSD-253').
Build a list of unique factor arrays across all assays.
Return a numbered menu as a markdown table.

Second call (selection='i,j,k,l,...,m,n'):

Pairs consecutive indices: (i,j), (k,l), ..., (m,n)
Must provide an even number of indices
For each pair, returns the matching assay(s) with technology, measurement, differential analysis method, and material columns so the assistant can pick the right assay for a downstream question (e.g., RNA-Seq for DE genes, WGBS for DM regions, amplicon for organism abundance) WITHOUT issuing a follow-up Cypher query.

Input Schema

Name	Required	Description
`study_id`	No
`selection`	No
`session_id`	No	Session id returned by `create_session()`. This server serves many users from one process; the session id is what keeps your output directory and generated plots private to you. Pass the SAME value on every tool call. If the server replies that the session is unknown or expired, call `create_session()` again and use the new id.

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedv1.0.0Oct 16, 2026

addedInput schema / properties / session_id

Added value: +{
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+  "description": "Session id returned by `create_session()`. This server serves many users from one process; the session id is what keeps your output directory and generated plots private to you. Pass the SAME value on every tool call. If the server replies that the session is unknown or expired, call `create_session()` again and use the new id.",
+  "title": "Session Id"
+}

changedOutput schema / (root)

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First observedv0.4.0May 29, 2026

TDQS

A4.8/5.0

Behavior5/5

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

Annotations only declare readOnly/idempotent/no-open-world; the description adds substantial non-structured behavior: a two-call stateful workflow (menu first, then indices), the even-number pairing requirement, the returned columns (technology/measurement/method/material) and the concrete loss from falling back to `query` (lost menu, lost per-match columns, lost next-step suggestions). This is well beyond what the annotations convey.

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?

Front-loaded with the routing decision and two clearly bulleted modes; every section is functional. Slight redundancy across the overlapping example phrasings ('What groups / conditions / control and experimental groups...') and the repeated query-fallback warning, but nothing is truly wasted.

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 carries the return-value burden and does so — it describes the numbered factor-menu markdown table, the per-assay comparison framing, and the per-match columns. Missing-`study_id` handling and the session-permission note are also covered, so an agent has everything needed to call it correctly.

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 only 33% (only `session_id` documented), so the description must compensate for `study_id` and `selection` — and it does, explaining the list-vs-resolve semantics of `selection` string ('2,1'), the even-index pairing rule, and study id examples ('OSD-48', 'OSD-253'). It stops short of a full format spec for `study_id`, so not a 5.

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?

States a specific verb+resource (list/select assays for a study) and immediately distinguishes itself from the sibling `query` tool ('USE THIS TOOL (not the `query` tool)'). Two distinct modes (list factor menu vs. resolve factor pair) are named with concrete examples, so an agent can tell it apart without opening the schema.

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?

Explicit when-to-use with quoted user phrasings, explicit when-not ('Never use `query` for this'), and two named alternatives-by-mode: call with just `study_id` for list mode, or with `study_id`+`selection` for resolution. The condition that selects each mode is unambiguous.

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

select_assays

Instructions

Input Schema

Schema Changelog

TDQS

Other Tools