get_annotation_confidence

Retrieve quality scores for UniProt protein annotations to assess reliability and support data-driven decisions in biological research.

Instructions

Quality scores for different annotations

Input Schema

TableJSON Schema

Name	Required	Description	Default
`accession`	Yes	UniProt accession number

Implementation Reference

src/index.ts:1778-1817 (handler)

The main handler function for the 'get_annotation_confidence' tool. Validates input, fetches UniProt protein data via API, extracts quality metrics like entryType, proteinExistence, annotationScore, evidence codes, review status, and reference count, then returns formatted JSON.

private async handleGetAnnotationConfidence(args: any) {
  if (!isValidProteinInfoArgs(args)) {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid annotation confidence arguments');
  }

  try {
    const response = await this.apiClient.get(`/uniprotkb/${args.accession}`, {
      params: { format: 'json' },
    });

    const protein = response.data;
    const confidenceInfo = {
      accession: protein.primaryAccession,
      entryType: protein.entryType,
      proteinExistence: protein.proteinExistence,
      annotationScore: protein.annotationScore || 'Not available',
      evidenceCodes: protein.features?.map((f: any) => f.evidences).flat().filter(Boolean) || [],
      reviewStatus: protein.entryType === 'UniProtKB reviewed (Swiss-Prot)' ? 'Reviewed' : 'Unreviewed',
      referenceCount: protein.references?.length || 0,
    };

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(confidenceInfo, null, 2),
        },
      ],
    };
  } catch (error) {
    return {
      content: [
        {
          type: 'text',
          text: `Error fetching annotation confidence: ${error instanceof Error ? error.message : 'Unknown error'}`,
        },
      ],
      isError: true,
    };
  }

src/index.ts:777-778 (registration)
Tool dispatch registration in the CallToolRequestSchema handler switch statement, routing calls to the specific handler function.
```
case 'get_annotation_confidence':
  return this.handleGetAnnotationConfidence(args);
```

src/index.ts:674-684 (registration)

Tool registration in the ListToolsRequestSchema response, defining name, description, and input schema.

{
  name: 'get_annotation_confidence',
  description: 'Quality scores for different annotations',
  inputSchema: {
    type: 'object',
    properties: {
      accession: { type: 'string', description: 'UniProt accession number' },
    },
    required: ['accession'],
  },
},

src/index.ts:677-683 (schema)

Input schema definition for the tool, specifying required 'accession' parameter of type string.

inputSchema: {
  type: 'object',
  properties: {
    accession: { type: 'string', description: 'UniProt accession number' },
  },
  required: ['accession'],
},

src/index.ts:79-89 (helper)

Input validation helper function used by the handler to check if arguments contain a valid accession (reused across multiple tools). Note: format validation is present but not used in this tool.

const isValidProteinInfoArgs = (
  args: any
): args is { accession: string; format?: string } => {
  return (
    typeof args === 'object' &&
    args !== null &&
    typeof args.accession === 'string' &&
    args.accession.length > 0 &&
    (args.format === undefined || ['json', 'tsv', 'fasta', 'xml'].includes(args.format))
  );
};

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