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Psilocin Human Neuron Transcriptomics

Read pathway results and sensitivities

get_transcriptomic_pathways
Read-onlyIdempotent

Search frozen pathway identifiers by literal substring (spaces become underscores). Returns all FGSEA variants and BOTH CAMERA settings where tested, including nonsignificant results. Paginate at most five pathways per call. Not independent replication.

Input Schema

NameRequiredDescriptionDefault
limitNo
queryNo
offsetNo
contrastNo

Output Schema

NameRequiredDescriptionDefault
dataYes
provenanceYes
atlas_linksYes
limitationsYes
field_definitionsYes

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.7/5.0
Behavior4/5

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

Annotations already cover the safety profile (read-only, idempotent, closed-world, non-destructive), and the description goes further by disclosing completeness behavior: all FGSEA variants, BOTH CAMERA settings where tested, nonsignificant results included, and the matching rule that spaces become underscores. The 'Not independent replication' caveat is a genuinely useful interpretation constraint that annotations cannot express; only the page-size cap merely restates 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.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Four short sentences, front-loaded with the core action and matching rule before the return behavior and the pagination constraint. Minor waste in 'Paginate at most five pathways per call', which duplicates the schema's maximum of 5.

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?

An output schema exists, yet the description still usefully summarizes return scope (all variants, both CAMERA settings, nonsignificant included) and states the non-replication caveat, which is enough for an agent to call it correctly. The remaining gap is parameter explanation for `contrast` and `offset`, which is a schema-side deficiency more than a description failure.

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 0%, so the description must carry parameter meaning, and it does explain the query matching semantics (literal substring, spaces to underscores) and the five-per-call page size. However, it says nothing about the `contrast` enum (day1/day3 comparisons) or what `offset` does, leaving two of four parameters undocumented anywhere.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description gives a specific verb and resource ('Search frozen pathway identifiers by literal substring') plus what comes back ('all FGSEA variants and BOTH CAMERA settings'). It is clearly distinguishable from search_transcriptomic_genes by being about pathway-level results, though it never names that sibling to sharpen the contrast.

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

Usage Guidelines3/5

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

Usage is only implied: an agent can infer this is the lookup for pre-computed pathway enrichment results, and the closing 'Not independent replication' warns against treating output as corroborating evidence. There is no explicit when-to-use statement and no routing to get_transcriptomic_gene, get_transcriptomic_robustness, or get_transcriptomic_provenance for adjacent questions.

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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