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Glama

Pombase

by io.github.pipeworx-io

Get Gene

get_gene
Read-onlyIdempotent

PomBase (fission yeast / S. pombe model-organism DB): look up a gene by its PomBase systematic id and return its product, protein domains (InterPro), deletion viability, UniProt id, and curation status. Keyless. NOTE: requires a systematic id like "SPAC1002.01" or "SPBC2F12.13" — standard gene names like "cdc2" are NOT resolved by this API. Complements SGD (budding yeast).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
idYesA PomBase systematic id, e.g. "SPAC1002.01" or "SPBC2F12.13". Standard names ("cdc2") are not accepted.

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

  1. Changed1 schema field changed
    • addedInput schema / examples
      Added value: +[
+  {
+    "id": "SPAC1002.01"
+  },
+  {
+    "id": "SPBC2F12.13"
+  }
+]
  2. First observed

TDQS

A4.7/5.0
Behavior4/5

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

Annotations indicate readOnlyHint, openWorldHint, idempotentHint, and destructiveHint false. The description adds context by stating it's keyless, requires a specific ID format, and lists return fields (product, domains, etc.), which is beyond the annotations.

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 with no extraneous information. The critical information (purpose, required format, exclusion of standard names, sibling relationship) is front-loaded.

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?

Despite no output schema, the description sufficiently outlines the return fields and constraints. For a simple lookup tool, it provides complete context for an agent to understand its function and limitations.

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%, and the description enhances the parameter documentation by reiterating the required format, providing examples, and noting that standard names are not accepted. The term 'Keyless' adds clarity.

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 explicitly states the tool looks up a gene by PomBase systematic id and returns specific fields like product, protein domains, deletion viability, etc. It also distinguishes itself from sibling tools by noting it complements SGD (budding yeast).

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?

The description clearly indicates when to use this tool (need a systematic id) and when not to (standard gene names are not resolved). It provides an explicit alternative (SGD) and gives examples of valid inputs.

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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TDQS

A3.8/5.0
Disambiguation2/5

Several tools have heavily overlapping purposes, notably ask_pipeworx vs ask_pipeworx_beta vs ask_pipeworx_grounded, and the cluster of polymarket tools covers adjacent prediction-market analysis territory. The PomBase-specific tools are distinct, but the overall set creates real selection ambiguity.

Naming Consistency3/5

Most names follow a readable snake_case style and many use verb-first patterns, but there is notable mixing: ask_pipeworx is a brand-style exception, entity_profile and polymarket_arbitrage are noun-first, and remember/recall/forget form an inconsistent trio. Not chaotic, but not a clean predictable convention.

Tool Count2/5

33 tools is excessive for a server named Pombase, where only get_gene and get_reference actually serve that domain. Even as a broad data-research server, the count is above the 25-tool threshold and includes many auxiliary utilities that feel bolted on rather than part of a focused surface.

Completeness2/5

The PomBase-specific coverage is severely thin: only systematic-ID gene lookup and PubMed-ID reference lookup, with no gene-name search, annotations browsing, phenotype data, or sequence access. The broader Pipeworx surface is extensive, but for the apparent Pombase purpose, agents will frequently hit dead ends.

Resources