Fetch Pfam protein domain annotations for a human transcript by providing its ENST identifier. Identify domain boundaries and associated missense tolerance data.
Signature: get_protein_domains(transcript_id, response_mode=).
| Name | Required | Description | Default |
|---|---|---|---|
| response_mode | No | Mode. | |
| transcript_id | Yes | ENST. |
| Name | Required | Description | Default |
|---|---|---|---|
No arguments | |||
Changes observed during successful MCP inspections.
v0.3.7Input 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"Input schema / properties / transcript_id / descriptionPrevious value: -"A versioned Ensembl transcript id (the .N version suffix is required), e.g. ENST00000269305.4. Resolve a gene symbol with resolve_transcript first."New value: +"ENST."Input schema / properties / transcript_id / examplesPrevious value: -[
- "ENST00000269305.4"
-]New value: +[
+ "ENST00000269305.9"
+]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": {
+ "properties": {
+ "domains": {
+ "additionalProperties": {
+ "items": {
+ "type": "integer"
+ },
+ "type": "array"
+ },
+ "type": "object"
+ }
+ },
+ "propertyNames": {
+ "pattern": "^(transcript_id|position|limit|offset|domains)$"
+ },
+ "type": "object"
+ },
+ "tool": {
+ "type": "string"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "^unsafe_for_clinical_use$": {
+ "const": true
+ }
+ },
+ "required": [
+ "tool",
+ "request_id",
+ "data_versions",
+ "unsafe_for_clinical_use"
+ ],
+ "type": "object"
+ }
+ },
+ "oneOf": [
+ {
+ "additionalProperties": false,
+ "patternProperties": {
+ "^(dropped_summary|transcript_id|recommended_citation)$": {
+ "type": "string"
+ },
+ "^_meta$": {
+ "$ref": "#/$defs/M"
+ },
+ "^domains$": {
+ "items": {
+ "additionalProperties": false,
+ "minProperties": 6,
+ "patternProperties": {
+ "^(ID|Name)$": {
+ "type": "string"
+ },
+ "^(start|stop|meta_domain_alignment_depth)$": {
+ "type": "integer"
+ },
+ "^metadomain$": {
+ "type": "boolean"
+ }
+ },
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "^gene_name$": {
+ "type": [
+ "string",
+ "null"
+ ]
+ },
+ "^success$": {
+ "const": true
+ }
+ },
+ "required": [
+ "success",
+ "_meta",
+ "transcript_id",
+ "domains",
+ "recommended_citation"
+ ]
+ },
+ {
+ "additionalProperties": false,
+ "patternProperties": {
+ "^(message|recovery_action|field|hint)$": {
+ "type": "string"
+ },
+ "^_meta$": {
+ "$ref": "#/$defs/M"
+ },
+ "^allowed_values$": {
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "^error_code$": {
+ "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"
- },
- "data_versions": {
- "additionalProperties": true,
- "type": "object"
- },
- "domains": {
- "items": {
- "additionalProperties": true,
- "properties": {
- "id": {
- "type": "string"
- },
- "meta_domain_alignment_depth": {
- "type": "integer"
- },
- "metadomain": {
- "type": "boolean"
- },
- "name": {
- "type": "string"
- },
- "start": {
- "type": "integer"
- },
- "stop": {
- "type": "integer"
- }
- },
- "type": "object"
- },
- "type": "array"
- },
- "error_code": {
- "type": "string"
- },
- "field": {
- "type": "string"
- },
- "gene_name": {
- "type": [
- "string",
- "null"
- ]
- },
- "hint": {
- "type": "string"
- },
- "message": {
- "type": "string"
- },
- "recommended_citation": {
- "type": "string"
- },
- "recovery_action": {
- "type": "string"
- },
- "retryable": {
- "type": "boolean"
- },
- "success": {
- "type": "boolean"
- },
- "transcript_id": {
- "type": "string"
- }
- },
- "required": [
- "success"
- ],
- "type": "object"
-}New value: +nullv0.1.0Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The readOnlyHint annotation is present, but the description adds no additional behavioral context (e.g., return format, side effects, required permissions). It does not contradict the annotation, but it also provides zero extra transparency.
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 extremely short, but it is not informative. It merely repeats the signature, which is redundant with the name and schema. It is concise in word count but fails to earn its place by adding any value.
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?
Given that the tool has an output schema and sits among related tools, the description lacks essential context such as what the output represents, typical usage scenarios, or any constraints. It is severely incomplete for an agent to understand how to call it correctly.
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?
Although schema coverage is 100%, the parameter descriptions are cryptic ('Mode.' and 'ENST.'). The tool description does not explain the meaning or usage of response_mode or transcript_id beyond the schema. The example value helps slightly for transcript_id, but overall the semantics are under-explained.
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 only a function signature, repeating the tool name and parameter list. It does not state what the tool does; the only clue is the name itself. This is essentially a restatement rather than a clear purpose.
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 on when to use this tool versus its siblings (e.g., get_meta_domain, summarize_intolerant_regions). The description provides no context for selection.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.