Resolve a query into a human transcript, retrieving missense tolerance, Pfam domain annotations, and variant counts from MetaDome.
Signature: resolve_transcript(query, response_mode=).
| Name | Required | Description | Default |
|---|---|---|---|
| query | Yes | Query. | |
| response_mode | No | Mode. |
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Changes observed during successful MCP inspections.
v0.3.7Input schema / properties / query / descriptionPrevious value: -"A gene symbol (e.g. TP53) or a versioned Ensembl transcript id (e.g. ENST00000269305.4). Gene symbols are resolved to candidate transcripts; a bare ENST id is validated and echoed."New value: +"Query."Input schema / properties / query / examplesPrevious value: -[
- "TP53",
- "ENST00000269305.4"
-]New value: +[
+ "TP53"
+]Input schema / properties / response_mode / defaultRemoved value: -"compact"Input schema / properties / response_mode / descriptionPrevious value: -"Verbosity: minimal|compact|standard|full (default compact)."New value: +"Mode."Input schema / properties / response_mode / typeRemoved value: -"string"Output schema / (root)Previous value: -nullNew value: +{
+ "$defs": {
+ "M": {
+ "additionalProperties": false,
+ "patternProperties": {
+ "^(tool|request_id|capabilities_version)$": {
+ "type": "string"
+ },
+ "^data_versions$": {
+ "additionalProperties": false,
+ "minProperties": 8,
+ "patternProperties": {
+ "^(assembly|gencode|uniprot|gnomad|clinvar|pfam|metadome_app|data_doi)$": {
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "^elapsed_ms$": {
+ "type": "integer"
+ },
+ "^next_commands$": {
+ "items": {
+ "additionalProperties": false,
+ "minProperties": 2,
+ "properties": {
+ "arguments": {
+ "propertyNames": {
+ "pattern": "^(query|transcript_id)$"
+ },
+ "type": "object"
+ },
+ "tool": {
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "^unsafe_for_clinical_use$": {
+ "const": true
+ }
+ },
+ "required": [
+ "tool",
+ "request_id",
+ "data_versions",
+ "unsafe_for_clinical_use"
+ ],
+ "type": "object"
+ }
+ },
+ "oneOf": [
+ {
+ "additionalProperties": false,
+ "oneOf": [
+ {
+ "properties": {
+ "resolved_from": {
+ "const": "id"
+ }
+ },
+ "required": [
+ "transcript_id"
+ ]
+ },
+ {
+ "properties": {
+ "resolved_from": {
+ "const": "gene"
+ }
+ },
+ "required": [
+ "gene_name",
+ "analyzable",
+ "transcripts"
+ ]
+ }
+ ],
+ "patternProperties": {
+ "^(dropped_summary|transcript_id|gene_name|note|recommended_citation)$": {
+ "type": "string"
+ },
+ "^_meta$": {
+ "$ref": "#/$defs/M"
+ },
+ "^analyzable$": {
+ "type": "boolean"
+ },
+ "^canonical_transcript_id$": {
+ "type": [
+ "string",
+ "null"
+ ]
+ },
+ "^resolved_from$": {
+ "enum": [
+ "gene",
+ "id"
+ ]
+ },
+ "^success$": {
+ "const": true
+ },
+ "^transcripts$": {
+ "items": {
+ "additionalProperties": false,
+ "minProperties": 6,
+ "patternProperties": {
+ "^(gencode_id|mane_transcript_type)$": {
+ "type": "string"
+ },
+ "^(has_protein_data|canonical)$": {
+ "type": "boolean"
+ },
+ "^aa_length$": {
+ "type": "integer"
+ },
+ "^refseq_ids$": {
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ }
+ },
+ "required": [
+ "success",
+ "_meta",
+ "resolved_from",
+ "recommended_citation"
+ ]
+ },
+ {
+ "additionalProperties": false,
+ "patternProperties": {
+ "^(message|recovery_action|field|hint)$": {
+ "type": "string"
+ },
+ "^_meta$": {
+ "$ref": "#/$defs/M"
+ },
+ "^allowed_values$": {
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "^candidates$": {
+ "items": {
+ "additionalProperties": false,
+ "minProperties": 1,
+ "properties": {
+ "transcript_id": {
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "^error_code$": {
+ "enum": [
+ "invalid_input",
+ "not_found",
+ "ambiguous_query",
+ "upstream_unavailable",
+ "rate_limited",
+ "internal"
+ ]
+ },
+ "^retryable$": {
+ "type": "boolean"
+ },
+ "^success$": {
+ "const": false
+ }
+ },
+ "required": [
+ "success",
+ "_meta",
+ "error_code",
+ "message",
+ "retryable",
+ "recovery_action"
+ ]
+ }
+ ],
+ "type": "object"
+}v0.3.1Output schema / (root)Previous value: -{
- "additionalProperties": true,
- "properties": {
- "_meta": {
- "additionalProperties": true,
- "type": "object"
- },
- "candidates": {
- "type": "array"
- },
- "canonical_transcript_id": {
- "type": [
- "string",
- "null"
- ]
- },
- "data_versions": {
- "additionalProperties": true,
- "type": "object"
- },
- "error_code": {
- "type": "string"
- },
- "field": {
- "type": "string"
- },
- "hint": {
- "type": "string"
- },
- "message": {
- "type": "string"
- },
- "query": {
- "type": "string"
- },
- "recommended_citation": {
- "type": "string"
- },
- "recovery_action": {
- "type": "string"
- },
- "retryable": {
- "type": "boolean"
- },
- "success": {
- "type": "boolean"
- },
- "total": {
- "type": "integer"
- },
- "transcripts": {
- "type": "array"
- }
- },
- "required": [
- "success"
- ],
- "type": "object"
-}New value: +nullv0.1.0Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The description adds no behavioral context beyond the annotation readOnlyHint: true. It does not mention what the operation does, what side effects it might have (though readOnly suggests none), or any additional behavioral constraints. With annotations present, the bar is lower, but the description still fails to add any value.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is a single line, which is concise, but it is under-specified rather than concise. It does not earn its place because it merely repeats the tool name and parameters, providing no additional information. It is not front-loaded with useful content; it is entirely placeholder.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
The tool has an output schema (indicated by 'Has output schema: true'), but the description does not explain what the output is or what the tool does. With two parameters and an output schema, the description is severely incomplete. An agent has no idea what 'resolve_transcript' means or what to expect as a result.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, so the baseline is 3. The description itself adds no parameter meaning—it only lists the parameter names. The schema already documents 'query' as a string with example 'TP53' and 'response_mode' as an enum, so the description does not need to compensate. It adds nothing, but baseline is acceptable.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description is merely a signature line, 'Signature: resolve_transcript(query, response_mode=).' It does not state what the tool does, what 'resolve_transcript' means, or what it returns. This is a tautology that restates the tool name and parameters without any purpose information.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
No guidance is given about when to use this tool versus any of the sibling tools. There is no mention of context, conditions, or alternatives. An agent has no way to know if this tool is appropriate for a given task.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.