Oliver's mTOR Atlas

Search entities

search_entities

Read-onlyIdempotent

Find genes/proteins, complexes, drugs, diseases, processes, nutrients and outcomes by name or synonym. Each result says where it matched (match_field: name, synonym or description); use match="name" to leave out description-only hits.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "query": "<query>"
    },
    "name": "search_entities"
  }
}

Input Schema

Name	Required	Description	Default
`type`	No	Optional type filter, e.g. "Drug", "Gene/Protein", "Disease"
`limit`	No	Maximum 100; a larger value is capped at 100.
`match`	No	"any" also searches descriptions; "name" searches names and synonyms only.	any
`query`	Yes	Name or synonym, e.g. "raptor", "sirolimus"
`offset`	No	For the next page: pass next_offset from the previous answer.

Schema Changelog

Changes observed during successful MCP inspections.

Changed2 schema fields changedOct 13, 2026
- addedInput schema / properties / limit / description
```
Added value: +"Maximum 100; a larger value is capped at 100."
```
- changedInput schema / properties / limit / maximum
```
Previous value: -100New value: +9007199254740991
```

Changed2 schema fields changedOct 13, 2026

addedInput schema / properties / match

Added value: +{
+  "default": "any",
+  "description": "\"any\" also searches descriptions; \"name\" searches names and synonyms only.",
+  "enum": [
+    "any",
+    "name"
+  ],
+  "type": "string"
+}

addedInput schema / properties / offset

Added value: +{
+  "default": 0,
+  "description": "For the next page: pass next_offset from the previous answer.",
+  "maximum": 9007199254740991,
+  "minimum": 0,
+  "type": "integer"
+}

First observedOct 1, 2026

TDQS

A4.2/5.0

Behavior4/5

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

Annotations already declare readOnly/idempotent/non-destructive/openWorld=false, so the safety profile is covered. The description adds genuinely new behavioral context: results carry a match_field indicating name, synonym, or description provenance, which is not derivable from the annotations or schema. It stops short of describing result ordering or pagination behavior beyond what the schema says.

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, zero filler, and the search scope is front-loaded before the result-shape and match-parameter guidance. Every clause adds information.

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?

For a read-only search with full annotation coverage and full schema descriptions, the description supplies the one thing the schema cannot: what the match_field in each result means. Pagination (next_offset) and the 100-result cap are already handled by the schema, so nothing critical is missing.

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%, so baseline is 3. The description goes beyond the schema by framing the match parameter's practical consequence ('leave out description-only hits') and by tying the returned match_field values back to the same name/synonym/description taxonomy, which helps an agent choose the parameter value intelligently.

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 (find genes/proteins, complexes, drugs, diseases, processes, nutrients, outcomes) and the matching basis (name or synonym). The enumerated entity types make it unmistakably distinct from search_authors and search_studies among the siblings.

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?

Gives one concrete usage rule (use match="name" to exclude description-only hits), which is a real when-to-use hint. However, it never states when to reach for this tool versus get_entity, find_relations, or the other search_* siblings — usage context is implied rather than explicit.

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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