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Glama

Emdb

by io.github.pipeworx-io

Search Maps

search_maps
Read-onlyIdempotent

Search the EBI Electron Microscopy Data Bank (EMDB) for 3D cryo-EM / electron-tomography density maps by free-text keyword (e.g. "ribosome", "spike protein", "apoptosis"). Returns matching maps with EMDB id, title, resolution (Angstrom), and structure-determination method. Keyless. Complements PDB/AlphaFold (which hold atomic/experimental structures).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNoMax results (default 15, max 50).
queryYesFree-text search, e.g. "ribosome", "spike protein".

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: +[
+  {
+    "query": "ribosome"
+  },
+  {
+    "limit": 25,
+    "query": "spike protein"
+  }
+]
  2. First observed

TDQS

A4.5/5.0
Behavior4/5

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

Annotations already declare readOnlyHint, openWorldHint, idempotentHint, destructiveHint=false. The description adds that it returns specific fields (EMDB id, title, resolution, method) and is 'keyless'. No additional disclosure needed beyond annotations; description adds context.

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?

Three sentences, each adding value: purpose, return fields, and comparison to alternatives. No wasted words. Front-loaded with action.

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 the annotations (readOnlyHint, openWorldHint, etc.) and full schema, the description covers all needed context: what is searched, returned fields, usage examples, and ecosystem fit. No output schema, but return values are described in text.

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 both 'query' and 'limit' described. The description adds example keywords and default/max for limit but does not significantly extend schema meaning. Baseline 3 is appropriate.

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 specifies 'Search the EBI Electron Microscopy Data Bank (EMDB) for 3D cryo-EM / electron-tomography density maps' with a clear verb and resource. It distinguishes from siblings like 'search_within' (searches within) and 'get_map' (retrieves specific map).

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 states 'Complements PDB/AlphaFold (which hold atomic/experimental structures)' and gives example keywords ('ribosome', 'spike protein'). It implies when to use this tool (for density maps) versus others. Explicit alternatives are provided.

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

A3.7/5.0
Disambiguation2/5

Multiple tool clusters have overlapping purposes: ask_pipeworx, ask_pipeworx_beta, and ask_pipeworx_grounded are near-identical (the beta is explicitly the same right now); five polymarket_* tools all surface opportunity/edge information; entity_profile, compare_entities, and recent_changes all cover company research. The descriptions are detailed, but an agent can easily misselect between similar tools.

Naming Consistency4/5

All tool names use consistent snake_case and are descriptive, with clear prefix patterns for prediction-market tools (polymarket_*) and the router variants (ask_pipeworx_*). Some names are verb-noun while others are noun-phrases, but the convention is uniformly underscore-separated, with no camelCase or other mixing.

Tool Count2/5

33 tools is excessive for a coherent server, and the scope is sprawled across EMDB access, Pipeworx data routing, prediction markets, memory, subscriptions, and miscellaneous utilities. Even though each tool has a defined role, the sheer breadth and number make it feel like several servers' worth of functionality crammed into one.

Completeness2/5

The server's name suggests it should be focused on EMDB, but only two tools (get_map, search_maps) cover that domain — no browsing, filtering, or extended metadata beyond basic fields. Meanwhile, the bulk of the surface is devoted to unrelated Pipeworx/platform features. For the stated purpose, the coverage is severely incomplete.

Resources