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Bioregistry

by io.github.pipeworx-io
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Read-onlyIdempotent

Search Bioregistry for biological database prefixes by substring match against prefix name, title, or description (e.g. "gene ontology"). Returns up to limit matching prefix records.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo
queryYes

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countYesTotal number of matches
queryYesThe search query
resultsYesMatching prefix entries

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed2 schema fields changed
    • changedOutput schema / properties / results / items / properties / description / type
      Previous value: -"string"New value: +[
+  "string",
+  "null"
+]
    • changedOutput schema / properties / results / items / properties / name / type
      Previous value: -"string"New value: +[
+  "string",
+  "null"
+]
  2. Changed2 schema fields changed
    • addedInput schema / examples
      Added value: +[
+  {
+    "query": "protein"
+  },
+  {
+    "limit": 10,
+    "query": "gene"
+  }
+]
    • changedOutput schema / (root)
      Previous value: -nullNew value: +{
+  "description": "Search results matching query",
+  "properties": {
+    "count": {
+      "description": "Total number of matches",
+      "type": "number"
+    },
+    "query": {
+      "description": "The search query",
+      "type": "string"
+    },
+    "results": {
+      "description": "Matching prefix entries",
+      "items": {
+        "properties": {
+          "description": {
+            "description": "Prefix description",
+            "type": "string"
+          },
+          "name": {
+            "description": "Prefix name",
+            "type": "string"
+          },
+          "prefix": {
+            "description": "Prefix identifier",
+            "type": "string"
+          }
+        },
+        "type": "object"
+      },
+      "type": "array"
+    }
+  },
+  "required": [
+    "query",
+    "count",
+    "results"
+  ],
+  "type": "object"
+}
  3. First observed

TDQS

A4.3/5.0
Behavior4/5

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

Annotations already disclose that the tool is read-only, idempotent, open-world, and non-destructive. The description adds value beyond these by explaining the substring matching behavior and the 'up to limit' result constraint, which are the operationally important traits an agent needs to call the tool correctly.

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 deliver all essential information: purpose, search target, matching strategy, example, and response bounding. There is no filler, and the main action is front-loaded.

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?

Given existing output schema, the description need not detail return fields. It is complete enough for an agent to call the tool with an arbitrary 'query' and optional 'limit'. It does not mention edge cases like case sensitivity or empty matches, but those are minor given the simplicity and existing schema.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description fully compensates for the missing property docs. It defines 'query' (substring matched against prefix name/title/description) and 'limit' (caps the number of returned records), directly answering what actual parameter semantics are. Both parameters are given concrete meaning.

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 states a specific verb and resource ('Search Bioregistry for biological database prefixes') and the matching mechanism ('by substring match against prefix name, title, or description'). This clearly differentiates it from sibling tools like 'prefix', 'prefixes', and 'search_within' without needing to inspect their schemas.

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?

The description conveys the search scope (Bioregistry prefixes) and gives an example query ('gene ontology'). However, it does not explicitly contrast with alternatives such as 'prefix' (exact lookup), 'prefixes' (list all), or 'search_within' (narrower search), so no clear guidance is provided on when to choose this over a sibling.

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

All Bioregistry toolsInspect
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